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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaatgtgcaaa...

Basic information

species Oryza sativa
transcript LOC_Os02g10070.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G064023_T04 (Zea mays), 5'ss of exon 6
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaat--gtgcaaa
||||||||||| ||||||||||||| |||||||||||||||||||||  | |||||||| || ||||||  |||| |  |         | ||| | ||  | ||||| |  | | |   | |   |  || || | || | ||||   ||  || |    || | ||
GTCCTTGGTGGAATGAGAGGGATGATTGGAATGCTTTGGGAAACATCCCTACTTGACCCAGAGGAGgtaatcttgcatgcatcctcttcatgatgctatgttagcatagtccata-gtgtactattagcttgtgcccat-tctatcaaaaatatgtacacagttccaa

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 5
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaatgtgcaaa-
||||||||||| ||||||||||| | ||||||||||||||| |||||  |  | ||||| || ||||||  | || |  |         | | | | ||  | ||||| | ||  |  |        |      |||| ||  |   ||       | | | |||| 
GTCCTTGGTGGAATGAGAGGGATCATTGGAATGCTTTGGGAGACATCCCTAGTCGACCCAGAGGAGgtaatcctgcatgcatcctcttcatggtgctatgttagcatagtgtactattatcagcttgtgcccattctacgtcaaaaatgtgtacacagt-tccaaat

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G063851_T04 (Zea mays), 5'ss of exon 6
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatt-tggatattttgtctatgtatatcttgaaattggaatgtgcaaa
||||||||||| |||||||||||||||||||||||||||||||||||  | ||||| || || ||||||  |||| || |         | ||| | ||  | ||||| | ||  |  |  |  ||   | | | | |    |||| |  |   |   |  |  || 
GTCCTTGGTGGAATGAGAGGGATGACTGGAATGCTTTGGGAAACATCCCTACTTGATCCAGAGGAGgtaatcttgcaagcatcctcttcatgatgctatgttagcatagtgtactattagctcgtgcccactctatgtcaaaatatgtacactgttccaaatttaa-

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 6
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaac-----tataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaatgtgcaaa-------------------
||  ||||||| |||||||||||||||||| ||||||||||||| ||||||||||||||||| ||||||    | |||       ||||  | ||| ||| | |  |   ||  || | |   ||  |   | ||  |     |   | |  | |   ||     |||||                    
GTTATTGGTGGAATGAGAGGGATGACTGGATTGCTTTGGGAAACCTCATTGCTTGACCCGGAAGAGgtac-tgtataactctctgtatatagttacaatagcttggttagatcctagatatagaatatatcaaatgctcctccttcctgttctaaggctgttg-atgcaattatcttatcattatttcag

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 5'ss of exon 5
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaattggaatgtgcaaa
|| |||||||| |||||||||||||||||| | || |||||||| |||||||||||  | ||||||||||| || |||  |  |   |   ||||   |   ||    || | |||  | | ||  |||   | |     ||| | ||| |   |           
GTACTTGGTGGAATGAGAGGGATGACTGGATTACTCTGGGAAACCTCATTGCTTGATGCAGATGAGgtatggttataattttgatcacatagataattttcaggtcagatcttgaattagaattatataacatatgatattatcttttgtatcag-----------

upper sequence: LOC_Os02g10070.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 6
GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgta----tgcttgtaaactataatgctacgataccataatggcataatatagaagcaaatttggatattttgtctatgtatatcttgaaatt--ggaatgtgcaaa----------------------------------------------------
|| |||||||| |||||||| ||||| ||  |||| |||||||| || ||||||||||| ||||| |||    | | | | |||   | |  |   |     | |||| ||  | |   |    ||||  ||   |  |  ||| || |   || ||   ||||  |    |                                                    
GTACTTGGTGGAATGAGAGGAATGACAGGGTTGCTGTGGGAAACCTCGTTGCTTGACCCAGATGAAgtaaatatcccttttaacc-cattcttgaaactttgttatgg-attcttttatattttattttaatgactgtttgatgaatgttgggacatgagggaagatttttatttttttttgggtttccaatttagttctgaaagttgagcttctgtttttcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58693317|gb|CK082004.1|CK082004
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|58695278|gb|CK083965.1|CK083965
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|29614058|gb|CB619071.1|CB619071
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|29667252|gb|CB663527.1|CB663527
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|88573691|gb|CI665460.1|CI665460
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|58658570|gb|CK047250.1|CK047250
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|58599089|gb|CK009617.1|CK009617
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|58611144|gb|CK038856.1|CK038856
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|29614020|gb|CB619033.1|CB619033
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|88400849|gb|CI616854.1|CI616854
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCT
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCT
EST: gi|58690828|gb|CK079515.1|CK079515
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
EST: gi|58678175|gb|CK066862.1|CK066862
EST:     GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAG                         GGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG
genomic: GAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 71 (downstream exon)
Score: 23

GTCCTTGGTGGGATGAGAGGGATGACTGGAATGCTTTGGGAAACATCATTGCTTGACCCGGATGAGgtatgcttgt ... tcctatccagGGTATTCGTTTTAGGGGTCTCTCGATTCCAGAGTGCCAGAAAGTGCTGCCGACAGCAGTTAAAGATGGGGAGCCTTTGCCTGAGGGTCTACTTTGGCTTC




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